I don't have issues with pY mining drills with fluids but have come up with a fix for the pumpjack crash with PyPH. Replace line 347 in control.lua of Actual Craft Time with the following:
if (entity.name:find("pumpjack") and entity.type:find("mining%-drill")) then
As it turns out, the py pumpjacks have an entity name that includes "pumpjack" and their entity type is an assembling machine, so this line was applying to the py pumpjacks due to only checking the entity name. Vanilla pumpjacks are called "pumpjack" and have a type of mining drill. By setting the if statement that's looking for pumpjacks and check if the type is mining drill, it will now be able to skip over the Pyanodons pumpjack assembling machines.